import os
from mytk import JoinImages

subID = 'CMULTIS' + '011-1'
dir ='/Users/schimmt/Multis/app/FileAssociation/MULTIS_trials/'

imod = 'CT' # choose one
imod = 'MRI' # choose one

modal = ['T1','FS']  # separate folders named T1, etc under CMULTIS dir
# segment = ['Upper', 'Lower'] #change to Whole for arm
segment = ['UL','LL'] # upper and lower leg
# segment = ['WA'] # whole arm
for mod in modal:
    for seg in segment:

        niftiDir = dir + subID + '/' + imod +'/nii_leg/' + mod + '/' + seg
        print niftiDir
        joinedFile = os.path.join(dir + subID + '/' + imod + '/nii_leg/', subID + '_' + seg + '_' + imod + '_' + mod + '_' + '.nii')	# change this to whatever you want

        Joined = JoinImages(niftiDir, joinedFile, reverse=True)

print 'Join completed.'